In the shadows
by Mylifeisajoke
Summary: Before anyone else can tell him, the Nine tails tells Naruto the reason the entire village hates him. And Naruto is not happy with the village or anyone in it. How will this affect the way Naruto turns out? And will Naruto get revenge on the village? Who can tell. Powerful, Dark Naruto and possible Harem. Rated M for violence, language and lemons.
1. A Change of Heart

In the shadows.

Author note: This is my first attempt at a story, it probably won't be very good at least for a while. I'm planning on making it pretty long (at least 100k words) but again first story, reviews with constructive criticism are appreciated. Hope at least some of you like it.

Thanks.

Disclaimer: I don't own Naruto.

Chapter 1. A change of heart.

The roars of an angry mob echoed through the night. The pitchforks and makeshift weapons wielded by the mob cast nightmarish and elongated shadows through the alley as they were illuminated in the light of hundreds of flickering torches. As the shadows flicked across the face of a small 12 year old boy who cowered in fear at the mercy of the angry mob. He had been careless. And now he was backed into the corner with no chance of escape. They would hurt him. Badly. And he could do nothing to stop them. Hate for the villagers and village that had made his life hell for his entire life was the only thing going through the boys mind as the crowd descended upon him and the beating began. Closing his eyes and shielding his face as best he could he just waited for it to end, and the chance to start plotting his revenge.

"Die you filthy demon" was the last thing he heard before he lost consciousness, the phrase puzzling him greatly.

 _-The following morning-_

As the early morning sun gently rose above the Konoha skyline, it bathed the sleeping city in its soothing light. Lighting up the faces on the Hokage rock and illuminating the Hokage tower in all of its glory. Light filtered in through the window of the elderly Hokage's office. Hiruzen Sarutobi, the "God of Shinobi" and current Hokage of the leaf bathed in the warmth of the suns rays. Cracking a wry smile and sighing, the Hokage turned back to the seemingly never-ending mound of paperwork sitting on his large desk. Sighing once more he reluctantly began his daily task of attempting to make a dent in the mountain of paperwork once again.

 _-elsewhere in Konoha-_

The warmth of the morning sun was slowly beginning to wake the sleeping village, its civilians and Ninja alike stirred from the realm of sleep to begin the daily life of a hidden village. Shinobi began filing in to the Hokage office and taking missions, bakers were baking, children were laughing and playing in the streets on the way to school and the day was promising to be pleasantly peaceful and warm.

Iruka Umino, one of the instructors at the Konoha ninja academy had just arrived at his classroom. Taking the roll he had already noticed a notable difference in the class. The students were unusually silent, well at least for a class of young children they had been. But no, the absence of an attempted prank of some kind and lack of noise was a clear indicator to Iruka of the absence of one Naruto Uzumaki. While this was not necessarily a bad thing in terms of his plan to actually teach the class today, he feared there had to be a significant reason for the eager to learn, yet fairly hopeless class clown to actually miss a lesson.

Iruka had not always liked Naruto. The other instructors had warned him of the child, and he had at first been unable to control, or even like the boy. His constant pranks and acting up had been a large thorn in Iruka's side during the early days of Naruto's education. However eventually the similarities between the two lead to a fairly strange teacher-student relationship. Iruka had lost his parents during the attack on the Leaf made by the Nine Tails. And growing up an orphan had been hard on the man, driving him to be the class clown. Just like Naruto now was for the same reason. The similarities between the two were high in number and yet, because of the different ways in which the Nine tails had affected the two, it had taken a long time for Iruka to accept Naruto. He knew what growing up an orphan was like, and knew he could have done more to help the young boy in his early life. But the fear and hate of the boy that had been instilled upon him by the council and hordes of angry civilians had clouded his judgement in those early days.

He had known about the constant torment the boy had been subject to from the civilians. Hell he had even taken part in the "punishment" dealt by the angry mobs to the small child. That kind of mob mentality had been hard to break for Iruka. He had hated Naruto immensely for a long time, and becoming his teacher didn't really change that hate. However once he had come to know and understand the boy, he realised how similar the two were, and understood the boys need for attention.

This mutual understanding between the two had lead to the strange relationship the two now shared.

Naruto still pranked Iruka constantly, and Iruka still yelled and got mad. And yet it was different to how it was before. Now although nothing had seemed to change, the two had a close bond that grew closer with every new prank or screaming fit. Iruka had convinced Naruto to take his schooling seriously, seeing the potential the boy held, and he allowed Naruto to keep up his pranks and guise as the class clown, as he now knew that it was the boys own method of coping with the unbearable pain and loneliness of growing up alone without parents. He understood the boys need for attention, and knew that the pranks were his way of getting the attention he craved, and as such did not stop the boy from his pranking. And because of this, he could now only assume that the boys absence from the class was because of some elaborate prank that he was attempting to pull. Realising that the class had been waiting for him to address them for some time while he had been thinking so hard, he sighed and turned back to the class to begin the lessons for today. Wondering what Naruto was planning now.

The boy in question was certainly planning something. But nothing along the lines of a simple "prank". He was out for revenge. And he would have it. His "fellow villagers" had crossed the line this time. He had never understood the hatred that almost the entire village felt for him. But now he vowed to himself that he would find out why they hated him so much. As far as he could tell he had done nothing to anger the whole village collectively. Sure he liked to pull pranks on people, but they were never harmful, all he wanted was for them to notice him, and for someone, anyone to be his friend.

The sun had now been up for an hour or so. But it was only now managing to reach into the dark alleyway that Naruto now lay in. And as the warm rays finally illuminated it enough for Naruto to look at the extent of the damage his hatred grew. His left leg was most definitely broken. It was bent at an unnatural angle, he couldn't move it and it had been throbbing since he was regained consciousness. His right looked to be in almost as bad shape, it was probably broken too just not to the gruesome extent of his left. Both were covered in bruises and covered in his own dried blood. It looked like he wouldn't be going to class today, or moving for that matter.

His arms were torn to shreds and covered in even more blood than his legs, they hung limply by his side but had served their purpose nonetheless. His head was still intact, which was a good sign, and his face was the least damaged part of his body at the sacrifice of his arms. He could move none of his limbs, and so he lay there plotting his revenge on the village that cared so little for him and had caused him so much pain.

 **Boy, you are pathetic.** The voice came from nowhere. No one else was in the alleyway. Or anywhere in the vicinity. But it had still been there. He had heard it before. Many times in his dreams, but still couldn't figure out its origins and normally just ignored it. But this time it continued and he could do nothing to stop it.

 **Why do you simply let those weaklings do that to you. I know you are pathetic, but still. Even someone as weak as you could decimate those weaklings.** The voice was deep and full of cunning and malice. And it was inside his head. How it got there and who it came from was a mystery to the boy. "Who are you and what do you want" was his immediate response. It seemed to have fallen on deaf ears however as the voice did not return for a long while.

 **I am the one who can grant you the power to destroy this village and everyone in it with the flick of your wrist. I can heal your wounds in a matter of seconds and give you enough power to crush them all like the insignificant bugs they are.**

"How could you give me that much power?" the boy asked in awe. His mind racing at the prospect of what he could do with as much power as the voice hinted at.

 **I am the reason for their hate boy. It is because of me that they have always hated you. I am the all powerful Nine Tails. And I will grant you the power to crush this village in its entirety on one condition.**

"Wait a second the fuck do they hate me because of you? The Fourth Hokage killed you before I was even born, why would they hate me because of you?" growled the boy angrily.

Menacing and maniacal laughter was the only response from the "Nine tails".

 **No one "kills" me boy. I am invincible and even that pathetic man knew that. Unfortunately for you he knew how to stop me. And thats why they all hate you so much.** **The day I was defeated was the day you were born boy. And I was defeated at the cost of that pathetic humans life and at yours.** The laughter began once again.

"What do you mean at the cost of my life, I'm still alive here asshole" The boy was getting more and more angry as the conversation progressed.

"Tell me everything you know. Now" Commanded the boy in his most assertive tone.

 **You do not tell me what to do you pathetic human. However I am going to tell you why the villagers hate you, only because it will drive you to hate them more, and then with my power you will crush them all.**

 **Your precious 4** **th** **Hokage was a fool. He knew he could not kill me, only seal me away. Which is where you come in. In order to save his precious village that fool sealed me away at the cost of his own life. Into his pathetic son. Into you. Thats right boy, your own father is the reason this village hates you so much. He sealed a demon into you and did nothing to stop the villagers from trying to kill the demon after his death. The Third Hokage never told you he was your father did he? He certainly didn't tell you that you have a demon inside of you. And yet he did nothing to stop the villagers from trying to kill you because of the demon inside of you. You have grown up an orphan because your idiot father killed himself trapping me inside of YOU. And your precious "grandpa Hokage" has done nothing to stop the villagers beating and despising you.**

"Why the fuck did the old man never tell me" screamed the boy.

"He should have fucking told me why they hated me, thats it this place is going down." The boy was filled with hatred at the village that had hated him his whole life for something his asshole of a father had done when he had just been born. "Give me your power you stupid fox. I want to destroy this place"

 **Naruto Uzumaki, you are too weak to destroy this village. I will grant you a portion of my power until your hatred is strong enough. Bide your time. Hide your power and pretend to not have changed. Train in the shadows and never reveal your full strength. And when the time comes I will grant you my full power and together we will crush this pathetic village and everyone in it.**

"Good idea. They wont suspect a thing if I hide my power and get stronger without their knowledge. Alright Nine Tails. Give me your power so that I can become stronger. I want to start now."

 **Alright boy, I will grant you one quarter of my power and heal you. Then you must follow my instructions to find a lair hidden in the village for you to train in secret.**

"Just give me your power already".

 **Fine. You insolent boy. Now listen closely and I will tell you how to find your new lair.**

End of Chapter 1.

Authors note: That probably wasn't the best introduction to the story I ca come up with, I will go back and edit it soon to make it better, but at the moment I'll continue with the story and get a few chapters out.


	2. The Lair

Chapter 2. The Lair.

As the sun reached the peak of its axis in the clear blue sky above Konoha, Naruto Uzumaki emerged from the shadows of a secluded alley. To anyone that knew the boy he seemed to be the same as ever, apart from a slight limp. His blank face masked the hatred and contempt he felt for all of those in the street nearby. Villagers stared and yelled insults as he walked through the bustling streets in the middle of the village, to no result as the boy simply stared straight ahead as he walked in the direction of the academy.

Had someone been following him they would have assumed he was just late for school, and heading there for his daily lessons. However as the streets narrowed and were dotted with fewer people nearer to the outskirts of the village where the academy was located, anyone that had been following would have been unable to. For Naruto Uzumaki had disappeared. 3 blocks from his supposed destination, the ninja academy.

Following the instructions of the voice in his head, Naruto had disappeared into yet another dark alleyway, leaving no trace of having been on the street, or entering the alley. The alley was bordered by two of the boarded up apartments that dotted the poorer area of the village. And almost invisible to the average eye was the entrance to what appeared to be a sewer. Dripping with mildew and certainly smelling of sewage, the damp, dark tunnel definitely didn't invite anyone inside it. However the voice in his head drove him to enter the rancid tunnel.

Filthy water dripped from the roof and the smell of sewage and rotting flesh hit Naruto as he entered, but he just covered his mount and nose with his sleeve and pushed on into the dark tunnel at the command of the voice in his head. The small trickle of oily black and fetid water that was flowing from the tunnel began to increase in volume and noise. Soon the water formed a small stream that spewed from the depths of the sewer tunnel and flowed past Naruto towards the exit. Still holding his sleeve over his nose to protect it from the assault of the foul smelling sever he continued to push on into the depths o the tunnel.

Naruto eventually reached the end of the tunnel, and a brick wall revealing the source of the disgusting stream of water being a small opening in the wall pouring fourth the foul water. The voice in his head told him what to do, and turning left he pressed his hand firmly against a loose and out of place looking brick in the wall. And like in any good movie a part of the wall swung open to reveal a hidden doorway into which Naruto cautiously entered.

Beyond the doorway a tunnel identical to the one he had just left (apart from the disgusting water) continued off into the darkness. However this time, Naruto flicked a switch and illuminated the tunnel allowing him a view of what he had stumbled upon, and eliciting a gasp from the young boy.

A vast, cavernous room spread out before him. Shelves of scrolls and books formed isles on the left hand side of the room and lined the walls, a large clear training field was set on the side opposite from Naruto. And to his right were what appeared to be basic living quarters for the previous inhabitant. A large king sized bed with a long rotten mattress was pushed neatly up against the bottom right hand corner of the room nearest to where Naruto stood. A small kitchen area with a simple stove and even a sink stood adjacent to the bed, and forming a sort of wall around the living quarters were rows and rows of shelves stacked with any kind of weapon that Naruto could imagine. Rows of shuriken, kunai, senbon and Swords of all sizes and shapes lined the shelves.

Naruto looked like he had just stumbled upon a gold mine, and in a way he had.

Up until a few hours ago, Naruto had never understood why the villagers hated him. He had never been able to afford any of the Ninja tools that lined these shelves. Every time he had attempted to buy kunai or shuriken, the shopkeepers of the various weapon stores would yell at him and refuse to sell him any weapons that "the demon would use to destroy the village" with. Now that he had access to a seemingly endless supply of these weapons, he could make the fears of the shopkeepers a reality. In time.

The voice in his head chuckled as a childlike grin spread across Naruto's face and he bolted into the room to explore and claim the hideout as his own. His first thought was to examine his new supply of weapons. The collection of weapons was extensive. Thousands of kunai and shuriken lined the shelves and although dusty and covered in cobwebs, the majority seemed to be unused and in very good condition. Naruto then searched the racks of swords and other larger ninja tools for a weapon that he could start training with. The shelves were lined with hundreds of dangerous and wicked looking katanas, machetes and tanto. Naruto inspected every one of them until he came to a very sharp looking machete. It was simple in design, but looked to be made of very high quality materials and looked like it could be very dangerous in the right hands. Removing it from the shelf and giving it a few practice swings Naruto decided to take the sword with him, with the option of choosing a different one later if he didn't like it. After all there were literally hundreds of other options lining the shelves that he stood by.

Returning the blade to its sheath and strapping it to his back, Naruto turned back to the kunai and shuriken. He grabbed handfuls of each and filled his weapons pouch with a generous supply of each. Then turning to the larger type of shuriken Naruto also grabbed two Fuuma shuriken and strapped them into place beside his new machete.

Naruto grinned at his new arsenal and turned back to survey his new living quarters properly. The large bed in the corner of the makeshift room looked like it had once been comfortable. Now however the mattress was completely rotten and looked like it would collapse under his weight. Naruto decided to replace the mattress at the first opportunity he could so that he could move in to this new hideout. The bed frame looked sturdy enough to hold a new mattress and multiple people on top of it if need be which also caused Naruto to grin. He then tested the sink to see if it provided a had a supply of running water, and after discovering that yes it did, and that the water was clean, and also drinkable. This was turning out to be is lucky day. He quickly surveyed the rest of the room. The Rug on the ground was also rotten but could be replaced, the sink worked, the bed needed a new mattress and the stove had a working source of gas and a large wardrobe in the corner opposite the bed allowed him a place to store any new cloths that he bought. Yes he thought to himself, this place was certainly liveable.

 **Naruto. Before you leave you must examine the library here. It has lots of jutsu that can make you much stronger. And the training ground needs to be repaired so that you can use that to practise your new jutsu and get stronger.** "Yeah, yeah relax nine tails I was just about to go check out the scrolls. Im not stupid you know" replied Naruto irritably. **Could have fooled me.** Was the retort he got back to which Naruto just snorted and walked over to the vast library of scrolls and Jutsu.

His eyes widened at the sheer number of scrolls that littered the shelves on the other side of the room. Skimming through the names of each scroll he soon realised that they were all sorted into categories. The first two shelves consisted of Maps, History books, laws of the village and various other things that were currently being taunt to him at the academy but to a much more extensive variety of information. He decided to go over them later to help develop a better knowledge of the world around him, knowing that reading everything on those shelves would make him much more intelligent and allow him to become much stronger. He then moved on to the next shelves. There seemed to be 6 separate shelves to house thousands of interesting looking Ninjutsu scrolls and techniques. He couldn't wait to start learning some of them but knew he needed to get stronger first. The next 3 shelves held scrolls outlying various different genjutsu's. And although he knew from personal experience that he definitely wasn't the best at genjutsu, the sheer number of scrolls here would make it much easier for him to learn at least a few basic genjutsu techniques.

He found 4 shelves of different Taijutsu style scrolls that intrigued him, as he considered himself to be a strong close combat fighter and therefore the thought of learning all of these new types of taijutsu styles intrigued him greatly. Another shelf over found a collection of Kenjutsu scrolls that could help him learn how wield his new machete much better. Another shelf revealed medical ninjutsu scrolls which although he thought could be useful he had little use for due to his newfound vastly increased healing powers thanks to the power granted to him by the Nine tails. He found that he had reached the opposite end of the large square cavern that housed the secret hideout and decided to more closely examine the scrolls on the last shelf of the library. The section seemed to be made up of Fuinjutsu scrolls which intrigued him because during his time at the academy he had heard of Fuinjutsu and had always wanted to try learning it, but never been able to find any scrolls on it. And so he rummaged through the scrolls looking for one that he could learn the basics from. The first scroll that he picked up seemed to call to him and draw him in.

Picking up the scroll that was titled "How to not suck at Fuinjutsu" Naruto flipped open the cover to read who the author was, and was shocked at the name. It read "The one and only, The Mighty, JIRAIYA!" Now this was also someone that he had heard of. Jiraiya was one of the great Sanin of the Leaf. Renown throughout the Land of Fire for his power, strength and pervertedness. Naruto sat down and began skimming through the book. It entailed the basics of Fuinjutsu or sealing Jutsu. Naruto knew that Jiraiya was a powerful ninja, and was known to posses powerful Fuinjutsu abilities. He also knew that Jiraiya had taught the 4th Hokage, who turned out to be Naruto's own father. His asshole of a father didn't become the Hokage for no reason though, and Naruto knew it. Minato Namikaze had been world renown as the "Yellow flash of the leaf". And Naruto knew that it was because of his special technique the Flying Thunder god. The technique that had made Minato world renowned as the fastest Shinobi in history had used Fuinjutsu to allow him to instantly teleport. And although he definitely didn't want to follow in his "noble and honourable" fathers footsteps, the technique was extremely powerful and Naruto definitely wanted to at least try and learn it. And so after skimming through the basics of the scroll Naruto tucked it away in his pocket to read later in more depth and stood back up to examine his new training field. He walked over to the large 10 by 10 meter square field. It was riddled with craters and scorch marks from the previous occupants training, and the walls around it were also scorched and chipped. It could however be easily repaired in time and Naruto knew that it would be invaluable in helping him study his new library of Jutsu and get much stronger. And so, grinning to himself once again Naruto turned from the field and walked back to the entrance. He once again surveyed his new hideout. Knowing that it would be his new home away from home before turning and leaving through the tunnel, locking the secret entrance once again to stop any other curious ninja from stumbling upon it.

Looking up at the sun in the sky Naruto realised that he had already missed 2 hours of class today and that he should get to the academy soon before he missed the rest of the days lessons and made Iruka sensei mad. Iruka had been pretty much the only person in the village that didn't hate him for no reason, and so Naruto had become fairly close with the man. Not wanting to disappoint Iruka, Naruto plastered his trademark grin onto his face and roof hopped his way to the nearby academy as fast as possible.

End of Chapter 2.

Authors note: These first couple chapters are fairly short, I know. I'm planning on making the later ones reach up to 10k words each. Next chapter Naruto makes it back to the academy, has a confrontation with Sasuke, shops for a mattress and gets a new wardrobe.


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